For 13 months, this study monitored the sedimentary organic matter composition, benthic bacteria and macrofauna at a permanent sampling station on the inner shelf (~ 40 m depth) near Ubatuba in SE Brazil. The sedimentary organic matter compounds were evaluated for total organic matter content, lipid biomarkers and phytopigments. The organic matter content varied significantly over time but no clear seasonal trend was evident. Lipid biomarker composition revealed that particulate organic matter was primarily derived from autochthonous sources, such as diatoms, other microalgae, zooplankton, sediment bacteria and benthic metazoan fauna. Phytopigment results revealed that the majority of the organic matter in the sediments was refractory as opposed to labile, suggesting that the labile portion is rapidly consumed. The benthic dynamics off the coast of Ubatuba is highly influenced by the intrusion of the South Atlantic Central Water (SACW) onto the shelf, which brings nutrients up to the euphotic zone and stimulates new phytoplanktonic production. This enhances the flux of organic matter to the bottom and increases benthic biota density, mainly bacteria. These results suggest a strong and complex benthic–pelagic coupling that is influenced by both mesoscale oceanographic events (i.e., intrusion of SACW) and local events (cold fronts) through remobilization of the sediments.